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In this paper,we consider the bipartite output tracking of heterogeneous linear multi-agent systems with a leader.Negative edge weights are introduced in modelling the communication graph between agents.LQR-based approach is used to derive the distributed protocol for the follower agent to achieve bipartite tracking of the leader.Two novel control protocols are proposed for cooperative output tracking of heterogeneous linear multi-agent systems,and this by itself contributes the literature of cooperative control of multi-agent systems.The modified protocols are then introduced to solve the bipartite output tracking of heterogeneous linear multi-agent systems,while the associated signed graph is structurally balanced and has a spanning tree with the leader as the root node.Numerical examples are given to show the effectiveness of our control protocols.